Quantitative Biology
Building on evidence of structural parallels between brain networks and the cosmic web [1], we apply AI-based geometric analysis to cultured neuronal networks. Isolated neurons self-organize into dendritic lattices shaped by reproducible…
The Language of Thought (LOT) hypothesis posits that at least some important cognitive processes involve language-like representations. These representations must be processed by appropriate hardware. Since the organ of biological cognition…
Building custom data analysis platforms traditionally requires extensive software engineering expertise, limiting accessibility for many researchers. Here, I demonstrate that modern large language models (LLMs) and autonomous coding agents…
Biology is at the precipice of a new era where AI accelerates and amplifies the ability to study how cells operate, organize, and work as systems, revealing why disease happens and how to correct it. Organizations globally are prioritizing…
Untargeted metabolomics using LC-MS/MS offers the potential to comprehensively profile the chemical diversity of biological samples. However, the process is fundamentally limited by the "identification bottleneck," where only a small…
European grapevine (\textit{Vitis vinifera} L.) is a climate-sensitive perennial whose flowering and ripening govern yield and quality. Phenological records from monitoring programs are typically collected at irregular intervals, so true…
Biological processes rely on finely tuned homo- and heteromeric interactions between (biomacro)molecules. The strength of an interaction, typically given by the dissociation constant (KD), plays a crucial role in basic research and must be…
Spiking neural networks (SNNs) are artificial neural networks based on simulated biological neurons and have attracted much attention in recent artificial intelligence technology studies. The dendrites in biological neurons have efficient…
The accurate identification of individuals from functional connectomes (FCs) is critical for advancing individualized assessments in neuropsychiatric research. Traditional methods, such as Pearson's correlation, have limitations in…
The inference of phylogenetic networks, which model complex evolutionary processes including hybridization and gene flow, remains a central challenge in evolutionary biology. Until now, statistically consistent inference methods have been…
We introduce AbBiBench (Antibody Binding Benchmarking), a benchmarking framework for antibody binding affinity maturation and design. Unlike previous strategies that evaluate antibodies in isolation, typically by comparing them to natural…
Tactile sensing remains far less understood in neuroscience and less effective in artificial systems compared to more mature modalities such as vision and language. We bridge these gaps by introducing a novel Encoder-Attender-Decoder (EAD)…
Ribonucleic acid (RNA) binds to molecules to achieve specific biological functions. While generative models are advancing biomolecule design, existing methods for designing RNA that target specific ligands face limitations in capturing…
The risk of mosquito-borne disease outbreaks is tightly linked to the frequency at which mosquitoes feed on blood, also known as the biting rate. However, standard models of mosquito-borne disease transmission inherently assume that…
Persistent homology applied to the activity of grid cells in the Medial Entorhinal Cortex suggests that this activity lies on a toroidal manifold. By analyzing real data and a simple model, we show that neural oscillations play a key role…
The iterative bleaching extends multiplexity (IBEX) Knowledge-Base is a central portal for researchers adopting IBEX and related 2D and 3D immunofluorescence imaging methods. The design of the Knowledge-Base is modeled after efforts in the…
Monod's law is a widely accepted phenomenology for bacterial growth. Since it has the same functional form as the Michaelis--Menten equation for enzyme kinetics, cell growth is often considered to be locally constrained by a single…
Biological evolution is realised through the same mechanisms of birth and death that underlie change in population density. The deep interdependence between ecology and evolution is well-established, and recent models focus on integrating…
One of the critical measures to control infectious diseases is a lockdown. Once past the lockdown stage in many parts of the world, the crucial question now concerns the effects of relaxing the lockdown and finding the best ways to…
Current non-invasive neuroimaging techniques trade off between spatial resolution and temporal resolution. While magnetoencephalography (MEG) can capture rapid neural dynamics and functional magnetic resonance imaging (fMRI) can spatially…